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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatttcacttacatataaactgtggggtaactttggatcttttggtcagcatcttacattcgagattcactaatcctatttgatattgcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG

Basic information

species Zea mays
transcript GRMZM2G149224_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 3'ss of exon 5
gtatggatttcacttacatataaactgtggggtaactttggatcttttggtcagcatcttacattcgagattcactaatcctatttgatattgctt--ttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG
                          ||  |||  |||     | |||   ||   | | |||  |  || ||  ||||  ||||   | ||  ||  ||| |||||||||||||||||||||||||| ||||||||||||||||||||||||| |||||||| ||||| || |||||||||||
--------------------------gtatggtcccttctttgcattt---cactttttaacaaccaggagtccataatattattgttttttatttgtttctagACCTATTTCATAACAAATATGGAGGCTATAAAATTCTGGGAGTTCATGTCGTTGATTTTGGAAGGACTCGGATATGAAAG

upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G14860.1 (Glycine max), 3'ss of exon 5
gtatggatttcacttacatataaactgtggggtaactt--tggatcttttggtcagca--tcttacattcga---gattcactaatcctatttgatattgcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG
         |    ||   || || | | |  |||  |  | ||| |    || || |   ||  || | |    | |    |  | |||    ||| |  ||||  || | ||||||||||||||||||||| |||| ||||| ||||||||| ||||| || |  | ||||||||||| |||||| |
---------tagactaagaatgaattattgcataaagtgattgatttgcaagttaggaaacctagcaattgctttggtattttcttgctaacatatacttgttttgtagGCATATTTCATAACAAATATGGAGTCTATGAAATTTTGGGAGTTCGTGTCAGTGGTAGTGGAAGGTCTTGGGTATGAAGG

upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G00480.1 (Glycine max), 3'ss of exon 5
gtatggatttcacttacatataaactgtggggtaactttggatcttttggtcagcatctt-----acattcgagattcactaatcctatttgatattgcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG
        |||   |||  |   |  | ||   |    | ||| |    || || |   |     |   | | |||    |  | |||   ||||||  ||||  || | |||||||||||||||||||| ||||| ||||| ||||||||| ||||| || |  | |||||||||||||||||| |
-------attcttctactaaaggaggggggaaaagtgattgatttgcaagttagaaaacttagcaattgttgtgatattttcttgctaacagatatttgttttgtagGCATATTTCATAACAAATATGGAACCTATGAAATTTTGGGAGTTCGTGTCAGTGGTAGTGGAAGGTCTTGGATATGAAGG

upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G24240.1 (Glycine max), 3'ss of exon 5
gtatggatttcacttacatataaactgtggggtaactttggatcttttggtcagca--tcttacattcgagattcactaatcctatt--tgatattgcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG
       |   ||| |   |             |    | ||| |    || |  |    |   | | |  ||    |  || |  |     ||||  ||||  || | |||||||||||||||||||||| ||| ||||| ||||||||||||| | || |  |  ||||||||||||||||| |
------ctcctactaaaggagggtaaaaaaaaaagtgattgatttgcaagttaagaaacatagaaattgctatggtattttcttgctaacattatttgttttgtagGCATATTTCATAACAAATATGGAGCTTATGAAATTTTGGGAGTTCATGTTAGTGGTAGTGAAAGGTCTTGGATATGAATG

upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G06080.1 (Glycine max), 3'ss of exon 5
gtatggatttcacttacatataaactgtggggtaactttggatcttttggtcagcatcttacattcgagattcactaatcctatttgatattgcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG
 | | | ||   |  |  | || |||| ||  |   |||| |  ||  ||  | |     |     | | |    |  | |||    |||||  ||||  || | |||||||||||||||||||||||||| ||||||||||||||| |||||||| |  | ||||||||||||||||||||
-tgttggttcttcacaggtgtatactggggaattgatttgcaagtta-ggaaacctagcaattgatgtggtattttgttgctaacaaatatttgttttgtagGCATATTTCATAACAAATATGGAGCCTATGAAATTCTGGGAGTTCGTGTCATTGGTAGTGGAAGGTCTTGGATATGAAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|87151705|gb|DY396494.1|DY396494
EST:     GAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAA                         ACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
genomic: GAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
EST: gi|18450805|gb|BM429083.1|BM429083
EST:     GAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAA                         ACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
genomic: GAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
EST: gi|149072461|gb|EE160738.2|EE160738
EST:     CGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAA                         ACCTATTCCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
genomic: CGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
EST: gi|22489855|gb|BU049778.1|BU049778
EST:     AAGATAGCCGCTGGAAAA                         ACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
genomic: AAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
EST: gi|31364547|gb|CD448902.1|CD448902
EST:     CGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAA                         ACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA
genomic: CGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 241

CTACTATGATTTCACCTACGTGGAAAATGTGGCATATGGCCATGTTTGTGCGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 236

CTACTATGATTTCACCTACGTGGAAAATGTGGCATATGGCCATGTTTGTGCGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

CTACTATGATTTCACCTACGTGGAAAATGTGGCATATGGCCATGTTTGTGCGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 308

CTACTATGATTTCACCTACGTGGAAAATGTGGCATATGGCCATGTTTGTGCGGAGAAAACTCTATCATCTGAAGATGGTGCAAAGATAGCCGCTGGAAAAgtatggattt ... gcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcagcatcttacattcgagattcactaatcctatttgatattgcttttccagACCTATTTCATAACAAATATGGAGCCTATAAAATTCTGGGAGTTCATGTCATTGATTTTAGAAGGTCTTGGATATGAAAG
                                           ttgcttttcc  CT-rich tract
                                  tatttgatatt  TA-rich tract